MILWAUKEE – There was a time when the Subway Series might have overshadowed the Yankees’ bigger issues, but those days are long gone, and this week’s crosstown showdown comes with the Yankees facing far more pressing concerns.

Namely, how can they improve their thinning rotation and inconsistent lineup?

On Sunday, the Yankees did what no other team had done this season: they scored a run off Brewers closer Francisco Rodriguez, and for just a moment that seemed to erase all other frustrations. But Mark Teixeira’s game-tying home run with two outs in the top of the ninth only delayed the inevitable as the Brewers rallied in the bottom of the inning to beat the Yankees 6-5 on a walk-off single.

“We were feeling really good about ourselves for a few minutes there,” Teixeira said.

Rodriguez, the former Mets reliever, had converted 15 straight save opportunities without allowing a run. He had two outs, a one-run lead and a full count against Teixeira, who sent a changeup into the seats for his team-leading seventh homer.

In the bottom of the inning, though, the Brewers got a broken-bat double that went just inside the first-base line. After a wild pitch, former Yankees third baseman Mark Reynolds hit the game-winner. Yankees reliever Adam Warren had been a strike away from getting out of the inning.

“It was a decent pitch,” Warren said. “But for 0-2 (in the count), feel like you’ve got to bury (the slider) more.”

Yankees starter David Phelps — one of three injury replacements currently in the rotation — had been terrific last time out, but this time he went five-plus innings with eight hits, three walks and four earned runs. He had a 3-2 lead heading into the sixth, but he and two relievers combined to give up three runs that inning. The Yankees had 11 hits, but again failed to capitalize on late scoring opportunities.

Now the Yankees have lost two straight and settled for a split on this six-game road trip when all three losses were perfectly winnable. Up next is the four-game Subway Series against the Mets, beginning with Monday’s game at Yankee Stadium.

It will be the final Mets matchup for Derek Jeter, who’s the only player remaining from the first Subway Series in 1997.

“It was all new (back then),” Jeter said. “You felt as though you had to win the series, like it was the World Series. It was all anyone was talking about. We lost the first game, and it was almost the end of the world. It was a long time ago. Now, it’s toned down a little bit, but it’s still fun for us as players. You want to win regardless of who you’re playing, but the atmosphere in the city was pretty special.”

Sabathia on DL

Six weeks into the season, the Yankees are on to their eighth starting pitcher, and the rotation that had been so encouraging out of spring training has already grown thin and uncertain.

The latest blow came on Sunday when Opening Day starter CC Sabathia was placed on the 15-day disabled list because of fluid in his right knee. The Yankees have already lost Michael Pineda to a shoulder injury and sent Ivan Nova for Tommy John surgery; 60 percent of their opening rotation is now on the DL.

“That’s why I didn’t want to say anything (about the knee),” Sabathia said. “But I think I was doing more damage to the team than helping the team by trying to hide it.”

Sabathia said he first felt the discomfort during last Sunday’s start against Tampa Bay. It was his worst start of the year, and his knee was swollen afterward. He stayed on turn to make another underwhelming start on Saturday, and when his knee grew swollen again, he finally spoke up and went for an MRI Sunday morning.

The problem is in the same knee that Sabathia had surgically repaired after the 2010 season. Although Sabathia said this injury is showing the same symptoms, the initial MRI suggests it’s less severe.

“There’s no meniscal tears,” manager Joe Girardi said. “I mean, that’s what our fear was because that’s what he’s had in the past. We’re hoping it will only be the two weeks. We just have to get it to calm down.”

Long reliever Alfredo Aceves has made two appearances out of the Yankees bullpen this season, and both came in games Sabathia started. Girardi called him the “leading candidate” to take Sabathia’s next scheduled start against the Mets on Thursday. Reliever Matt Daley was promoted from Triple-A to immediately fill Sabathia’s spot on the roster, but it’s worth noting that prospect Chase Whitley was scratched from a scheduled Triple-A start on Sunday afternoon. He could eventually come up to replace Aceves as the long man.

“The deepest organizations, the deepest teams, end up on top,” Mark Teixeira said. “We’ll see how deep we are and who’s going to step up.”

Already the Yankees have moved David Phelps and Vidal Nuno from the bullpen to the rotation, and they’ve burned through a series of long men — from Bruce Billings to Shane Greene to Chris Leroux — trying to keep pace with the evolving pitching needs.

Nova is lost for the year, Pineda isn’t expected back until June, and now Sabathia will miss at least two weeks.

“Obviously it tests your depth and it stretches you,” Girardi said.

Sabathia’s season was already a source of frustration before Sunday’s revelation. The team’s supposed-to-be ace is 3-4 with a 5.28 ERA through eight starts. He’s allowed 10 home runs already, including three on Saturday. He’ll have his knee drained on Monday in hopes of returning in two weeks with much better results.

“I’m not going to make excuses or anything, but I felt it (Saturday), and I just wanted to say something and let (the training staff) know,” Sabathia said. “. . . We’ll see what the doctor says, get another assessment and go from there.”